\section{NFcore::Molecule Class Reference}
\label{classNFcore_1_1Molecule}\index{NFcore::Molecule@{NFcore::Molecule}}
{\tt \#include $<$NFcore.hh$>$}



\subsection{Detailed Description}
Each molecule in the system is represented by an instance of this. 

The base unit of the NFsim program, this class maintains instances of individual objects that exist in the simulation. Molecules are able to interact with their \doxyref{MoleculeType}{p.}{classNFcore_1_1MoleculeType} so that they also 'know' about the reactions and observables they need to keep updated as they react and change states. There are also two static functions which are used to create and delete bonds (bind and unbind). \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\subsection*{Public Member Functions}
\begin{CompactItemize}
\item 
{\bf Molecule} ({\bf MoleculeType} $\ast${\bf parentMoleculeType}, int {\bf listId})
\item 
{\bf $\sim$Molecule} ()
\item 
int {\bf getMolListId} () const 
\item 
string {\bf getMoleculeTypeName} () const 
\item 
{\bf MoleculeType} $\ast$ {\bf getMoleculeType} () const 
\item 
int {\bf getUniqueID} () const 
\item 
void {\bf setComplexID} (int currentComplex)
\item 
int {\bf getComplexID} () const 
\item 
{\bf Complex} $\ast$ {\bf getComplex} () const 
\item 
int {\bf getDegree} ()
\item 
int {\bf getComponentState} (int cIndex) const 
\item 
int {\bf getComponentIndexOfBond} (int cIndex) const 
\item 
void {\bf setComponentState} (int cIndex, int newValue)
\item 
void {\bf setComponentState} (string cName, int newValue)
\item 
void {\bf setLocalFunctionValue} (double newValue, int localFunctionIndex)
\item 
double {\bf getLocalFunctionValue} (int localFunctionIndex)
\item 
void {\bf setUpLocalFunctionList} ()
\item 
bool {\bf isBindingSiteOpen} (int bIndex) const 
\item 
bool {\bf isBindingSiteBonded} (int bIndex) const 
\item 
{\bf Molecule} $\ast$ {\bf getBondedMolecule} (int bSiteIndex) const 
\item 
int {\bf getRxnListMappingId} (int rxnIndex) const 
\item 
void {\bf setRxnListMappingId} (int rxnIndex, int {\bf rxnListMappingId})
\item 
void {\bf setBondTo} ({\bf Molecule} $\ast$m2, int bindingSiteIndex)
\item 
void {\bf moveToNewComplex} (int newComplexID)
\item 
void {\bf traverseBondedNeighborhood} (list$<$ {\bf Molecule} $\ast$ $>$ \&members, int traversalLimit)
\item 
void {\bf prepareForSimulation} ()
\item 
void {\bf updateRxnMembership} ()
\item 
void {\bf removeFromObservables} ()
\item 
void {\bf addToObservables} ()
\item 
void {\bf updateTypeIIFunctions} ()
\item 
void {\bf updateDORRxnValues} ()
\item 
void {\bf printDetails} () const 
\item 
bool {\bf isObs} (int oIndex) const 
\item 
void {\bf setIsObs} (int oIndex, bool isObs)
\end{CompactItemize}
\subsection*{Static Public Member Functions}
\begin{CompactItemize}
\item 
static void {\bf bind} ({\bf Molecule} $\ast$m1, int cIndex1, {\bf Molecule} $\ast$m2, int cIndex2)
\item 
static void {\bf bind} ({\bf Molecule} $\ast$m1, string compName1, {\bf Molecule} $\ast$m2, string compName2)
\item 
static void {\bf unbind} ({\bf Molecule} $\ast$m1, int bSiteIndex)
\item 
static void {\bf unbind} ({\bf Molecule} $\ast$m1, char $\ast$bSiteName)
\item 
static void {\bf breadthFirstSearch} (list$<$ {\bf Molecule} $\ast$ $>$ \&members, {\bf Molecule} $\ast$m, int depth)
\item 
static void {\bf printMoleculeList} (list$<$ {\bf Molecule} $\ast$ $>$ \&members)
\item 
static int {\bf getUniqueIdCount} ()
\end{CompactItemize}
\subsection*{Public Attributes}
\begin{CompactItemize}
\item 
bool {\bf hasVisitedMolecule}
\item 
bool {\bf hasEvaluatedMolecule}
\end{CompactItemize}
\subsection*{Static Public Attributes}
\begin{CompactItemize}
\item 
static const int {\bf NOT\_\-IN\_\-RXN} = -1
\item 
static const int {\bf NOSTATE} = -1
\item 
static const int {\bf NOBOND} = 0
\item 
static const int {\bf NOINDEX} = -1
\end{CompactItemize}
\subsection*{Protected Attributes}
\begin{CompactItemize}
\item 
bool {\bf isPrepared}
\item 
int {\bf ID\_\-complex}
\item 
int {\bf ID\_\-type}
\item 
int {\bf ID\_\-unique}
\item 
int {\bf listId}
\item 
{\bf MoleculeType} $\ast$ {\bf parentMoleculeType}
\item 
bool {\bf useComplex}
\item 
int $\ast$ {\bf component}
\item 
int {\bf numOfComponents}
\item 
{\bf Molecule} $\ast$$\ast$ {\bf bond}
\item 
int $\ast$ {\bf indexOfBond}
\item 
double $\ast$ {\bf localFunctionValues}
\item 
bool $\ast$ {\bf isObservable}
\item 
int $\ast$ {\bf rxnListMappingId}
\item 
int {\bf nReactions}
\end{CompactItemize}
\subsection*{Static Protected Attributes}
\begin{CompactItemize}
\item 
static int {\bf uniqueIdCount} = 0
\end{CompactItemize}


\subsection{Constructor \& Destructor Documentation}
\index{NFcore::Molecule@{NFcore::Molecule}!Molecule@{Molecule}}
\index{Molecule@{Molecule}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}Molecule::Molecule ({\bf MoleculeType} $\ast$ {\em parentMoleculeType}, int {\em listId})}\label{classNFcore_1_1Molecule_09f19b608d8bcc051b61e2ab1fffa207}


\index{NFcore::Molecule@{NFcore::Molecule}!$\sim$Molecule@{$\sim$Molecule}}
\index{$\sim$Molecule@{$\sim$Molecule}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}Molecule::$\sim$Molecule ()}\label{classNFcore_1_1Molecule_1ff980b574a62526abff3d631c83bf94}




\subsection{Member Function Documentation}
\index{NFcore::Molecule@{NFcore::Molecule}!getMolListId@{getMolListId}}
\index{getMolListId@{getMolListId}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int NFcore::Molecule::getMolListId () const\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_5b8fa63376968f8905e7979e8648647b}


\index{NFcore::Molecule@{NFcore::Molecule}!getMoleculeTypeName@{getMoleculeTypeName}}
\index{getMoleculeTypeName@{getMoleculeTypeName}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}string NFcore::Molecule::getMoleculeTypeName () const\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_54b335a50f427d3af013b3f833552c78}


\index{NFcore::Molecule@{NFcore::Molecule}!getMoleculeType@{getMoleculeType}}
\index{getMoleculeType@{getMoleculeType}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf MoleculeType}$\ast$ NFcore::Molecule::getMoleculeType () const\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_7b3552809de0a478b64c4eb4ca4096d5}


\index{NFcore::Molecule@{NFcore::Molecule}!getUniqueID@{getUniqueID}}
\index{getUniqueID@{getUniqueID}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int NFcore::Molecule::getUniqueID () const\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_bdc033d5a74f5453712ac9ec36b0564f}


\index{NFcore::Molecule@{NFcore::Molecule}!setComplexID@{setComplexID}}
\index{setComplexID@{setComplexID}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void NFcore::Molecule::setComplexID (int {\em currentComplex})\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_69465045c57bb005157fc2aea3efb39d}


\index{NFcore::Molecule@{NFcore::Molecule}!getComplexID@{getComplexID}}
\index{getComplexID@{getComplexID}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int NFcore::Molecule::getComplexID () const\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_16f3f77ac1f62468a6f77be13f224b2b}


\index{NFcore::Molecule@{NFcore::Molecule}!getComplex@{getComplex}}
\index{getComplex@{getComplex}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf Complex}$\ast$ NFcore::Molecule::getComplex () const\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_42b4fdfe04c8da86bfd2ac5f4a93492d}


\index{NFcore::Molecule@{NFcore::Molecule}!getDegree@{getDegree}}
\index{getDegree@{getDegree}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int Molecule::getDegree ()}\label{classNFcore_1_1Molecule_390f0d1223bdd2ab075b25993902a520}


\index{NFcore::Molecule@{NFcore::Molecule}!getComponentState@{getComponentState}}
\index{getComponentState@{getComponentState}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int NFcore::Molecule::getComponentState (int {\em cIndex}) const\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_7b79c8463c9c4dc88549aa74ba7179cc}


\index{NFcore::Molecule@{NFcore::Molecule}!getComponentIndexOfBond@{getComponentIndexOfBond}}
\index{getComponentIndexOfBond@{getComponentIndexOfBond}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int NFcore::Molecule::getComponentIndexOfBond (int {\em cIndex}) const\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_644b32b9f8609ee675f2ecc4f458d678}


\index{NFcore::Molecule@{NFcore::Molecule}!setComponentState@{setComponentState}}
\index{setComponentState@{setComponentState}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::setComponentState (int {\em cIndex}, int {\em newValue})}\label{classNFcore_1_1Molecule_0eb79f69d465c6407b078f59465d1413}


\index{NFcore::Molecule@{NFcore::Molecule}!setComponentState@{setComponentState}}
\index{setComponentState@{setComponentState}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::setComponentState (string {\em cName}, int {\em newValue})}\label{classNFcore_1_1Molecule_7e96ad7ebb9ebde9324b1f069f8078d4}


\index{NFcore::Molecule@{NFcore::Molecule}!setLocalFunctionValue@{setLocalFunctionValue}}
\index{setLocalFunctionValue@{setLocalFunctionValue}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::setLocalFunctionValue (double {\em newValue}, int {\em localFunctionIndex})}\label{classNFcore_1_1Molecule_d5f5d4f6094fc06d21ee7834dd1d6ca5}


\index{NFcore::Molecule@{NFcore::Molecule}!getLocalFunctionValue@{getLocalFunctionValue}}
\index{getLocalFunctionValue@{getLocalFunctionValue}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}double Molecule::getLocalFunctionValue (int {\em localFunctionIndex})}\label{classNFcore_1_1Molecule_10dc17ce9638bbfe58693a428c95e3a8}


\index{NFcore::Molecule@{NFcore::Molecule}!setUpLocalFunctionList@{setUpLocalFunctionList}}
\index{setUpLocalFunctionList@{setUpLocalFunctionList}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::setUpLocalFunctionList ()}\label{classNFcore_1_1Molecule_74b2a51b8799923556e413a4955a3926}


\index{NFcore::Molecule@{NFcore::Molecule}!isBindingSiteOpen@{isBindingSiteOpen}}
\index{isBindingSiteOpen@{isBindingSiteOpen}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}bool Molecule::isBindingSiteOpen (int {\em bIndex}) const}\label{classNFcore_1_1Molecule_80db66e3d3582f040a363fc625130a88}


\index{NFcore::Molecule@{NFcore::Molecule}!isBindingSiteBonded@{isBindingSiteBonded}}
\index{isBindingSiteBonded@{isBindingSiteBonded}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}bool Molecule::isBindingSiteBonded (int {\em bIndex}) const}\label{classNFcore_1_1Molecule_4e50fb96e3a9cbd47d8ae7156f2a10bc}


\index{NFcore::Molecule@{NFcore::Molecule}!getBondedMolecule@{getBondedMolecule}}
\index{getBondedMolecule@{getBondedMolecule}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf Molecule} $\ast$ Molecule::getBondedMolecule (int {\em bSiteIndex}) const}\label{classNFcore_1_1Molecule_7833785f509d95b6a97b299526d1d6e4}


\index{NFcore::Molecule@{NFcore::Molecule}!getRxnListMappingId@{getRxnListMappingId}}
\index{getRxnListMappingId@{getRxnListMappingId}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int NFcore::Molecule::getRxnListMappingId (int {\em rxnIndex}) const\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_a352c3ff40bb38555c772124de0f0ac8}


\index{NFcore::Molecule@{NFcore::Molecule}!setRxnListMappingId@{setRxnListMappingId}}
\index{setRxnListMappingId@{setRxnListMappingId}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void NFcore::Molecule::setRxnListMappingId (int {\em rxnIndex}, int {\em rxnListMappingId})\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_9cf1eae438fc06f9e70d541e4a0b32d5}


\index{NFcore::Molecule@{NFcore::Molecule}!setBondTo@{setBondTo}}
\index{setBondTo@{setBondTo}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void NFcore::Molecule::setBondTo ({\bf Molecule} $\ast$ {\em m2}, int {\em bindingSiteIndex})}\label{classNFcore_1_1Molecule_83f24f5163f0521e1ce77bb8aef2ac97}


\index{NFcore::Molecule@{NFcore::Molecule}!moveToNewComplex@{moveToNewComplex}}
\index{moveToNewComplex@{moveToNewComplex}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void NFcore::Molecule::moveToNewComplex (int {\em newComplexID})\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_691daed6bab7b13dd5bfe6da41a8ab48}


\index{NFcore::Molecule@{NFcore::Molecule}!bind@{bind}}
\index{bind@{bind}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::bind ({\bf Molecule} $\ast$ {\em m1}, int {\em cIndex1}, {\bf Molecule} $\ast$ {\em m2}, int {\em cIndex2})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1Molecule_776a89ff6affb64d02f180403207d0ac}


\index{NFcore::Molecule@{NFcore::Molecule}!bind@{bind}}
\index{bind@{bind}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::bind ({\bf Molecule} $\ast$ {\em m1}, string {\em compName1}, {\bf Molecule} $\ast$ {\em m2}, string {\em compName2})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1Molecule_7a43a97c3f1baad5eb5e11b91683d782}


\index{NFcore::Molecule@{NFcore::Molecule}!unbind@{unbind}}
\index{unbind@{unbind}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::unbind ({\bf Molecule} $\ast$ {\em m1}, int {\em bSiteIndex})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1Molecule_e37cae25c4e0e544ae0b9b9930ae309b}


\index{NFcore::Molecule@{NFcore::Molecule}!unbind@{unbind}}
\index{unbind@{unbind}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::unbind ({\bf Molecule} $\ast$ {\em m1}, char $\ast$ {\em bSiteName})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1Molecule_b29bc47ee1304d31173dc00af20bbafd}


\index{NFcore::Molecule@{NFcore::Molecule}!traverseBondedNeighborhood@{traverseBondedNeighborhood}}
\index{traverseBondedNeighborhood@{traverseBondedNeighborhood}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::traverseBondedNeighborhood (list$<$ {\bf Molecule} $\ast$ $>$ \& {\em members}, int {\em traversalLimit})}\label{classNFcore_1_1Molecule_410a708dc5a802794c49a1b547e220cb}


\index{NFcore::Molecule@{NFcore::Molecule}!breadthFirstSearch@{breadthFirstSearch}}
\index{breadthFirstSearch@{breadthFirstSearch}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::breadthFirstSearch (list$<$ {\bf Molecule} $\ast$ $>$ \& {\em members}, {\bf Molecule} $\ast$ {\em m}, int {\em depth})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1Molecule_6242f0f2226f92690f67d2d60e39209e}


\index{NFcore::Molecule@{NFcore::Molecule}!prepareForSimulation@{prepareForSimulation}}
\index{prepareForSimulation@{prepareForSimulation}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::prepareForSimulation ()}\label{classNFcore_1_1Molecule_e7791ea7d5c718e769355885264ed27c}


\index{NFcore::Molecule@{NFcore::Molecule}!updateRxnMembership@{updateRxnMembership}}
\index{updateRxnMembership@{updateRxnMembership}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::updateRxnMembership ()}\label{classNFcore_1_1Molecule_418a61a3ccd7c37c53e30cbe90d35a94}


\index{NFcore::Molecule@{NFcore::Molecule}!removeFromObservables@{removeFromObservables}}
\index{removeFromObservables@{removeFromObservables}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::removeFromObservables ()}\label{classNFcore_1_1Molecule_b996dfd73160b4e2e0f060db729663c8}


\index{NFcore::Molecule@{NFcore::Molecule}!addToObservables@{addToObservables}}
\index{addToObservables@{addToObservables}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::addToObservables ()}\label{classNFcore_1_1Molecule_e971b5fde9399fab335e572c02ba253b}


\index{NFcore::Molecule@{NFcore::Molecule}!updateTypeIIFunctions@{updateTypeIIFunctions}}
\index{updateTypeIIFunctions@{updateTypeIIFunctions}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::updateTypeIIFunctions ()}\label{classNFcore_1_1Molecule_6339cd45a1ebb484a93bec719a2d0c76}


\index{NFcore::Molecule@{NFcore::Molecule}!updateDORRxnValues@{updateDORRxnValues}}
\index{updateDORRxnValues@{updateDORRxnValues}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::updateDORRxnValues ()}\label{classNFcore_1_1Molecule_2ed78fda19237bbfdc179530cce22e27}


\index{NFcore::Molecule@{NFcore::Molecule}!printDetails@{printDetails}}
\index{printDetails@{printDetails}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::printDetails () const}\label{classNFcore_1_1Molecule_ac8b6c3431849b5b10af61ebb37f0535}


\index{NFcore::Molecule@{NFcore::Molecule}!printMoleculeList@{printMoleculeList}}
\index{printMoleculeList@{printMoleculeList}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void Molecule::printMoleculeList (list$<$ {\bf Molecule} $\ast$ $>$ \& {\em members})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1Molecule_6773f433bfb5546ddc0e8546aaec9817}


\index{NFcore::Molecule@{NFcore::Molecule}!getUniqueIdCount@{getUniqueIdCount}}
\index{getUniqueIdCount@{getUniqueIdCount}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}static int NFcore::Molecule::getUniqueIdCount ()\hspace{0.3cm}{\tt  [inline, static]}}\label{classNFcore_1_1Molecule_e11f21aabfaa393b34f680bbbee6b20d}


\index{NFcore::Molecule@{NFcore::Molecule}!isObs@{isObs}}
\index{isObs@{isObs}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}bool NFcore::Molecule::isObs (int {\em oIndex}) const\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_c860910b0fd0df5730577c236fc1b890}


\index{NFcore::Molecule@{NFcore::Molecule}!setIsObs@{setIsObs}}
\index{setIsObs@{setIsObs}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void NFcore::Molecule::setIsObs (int {\em oIndex}, bool {\em isObs})\hspace{0.3cm}{\tt  [inline]}}\label{classNFcore_1_1Molecule_1799a19c9b9c93d31266757ad37373b5}




\subsection{Member Data Documentation}
\index{NFcore::Molecule@{NFcore::Molecule}!NOT\_\-IN\_\-RXN@{NOT\_\-IN\_\-RXN}}
\index{NOT\_\-IN\_\-RXN@{NOT\_\-IN\_\-RXN}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const int {\bf NFcore::Molecule::NOT\_\-IN\_\-RXN} = -1\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1Molecule_b17b0ab2e0bd3746c065351e346f4ffe}


\index{NFcore::Molecule@{NFcore::Molecule}!hasVisitedMolecule@{hasVisitedMolecule}}
\index{hasVisitedMolecule@{hasVisitedMolecule}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}bool {\bf NFcore::Molecule::hasVisitedMolecule}}\label{classNFcore_1_1Molecule_e828ebe80d90495cb772bde29177166e}


\index{NFcore::Molecule@{NFcore::Molecule}!hasEvaluatedMolecule@{hasEvaluatedMolecule}}
\index{hasEvaluatedMolecule@{hasEvaluatedMolecule}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}bool {\bf NFcore::Molecule::hasEvaluatedMolecule}}\label{classNFcore_1_1Molecule_ea3516e9686a0b8f2ee867956cc31c3c}


\index{NFcore::Molecule@{NFcore::Molecule}!NOSTATE@{NOSTATE}}
\index{NOSTATE@{NOSTATE}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const int {\bf NFcore::Molecule::NOSTATE} = -1\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1Molecule_6909d5d11595ba857c28e382a81526b8}


\index{NFcore::Molecule@{NFcore::Molecule}!NOBOND@{NOBOND}}
\index{NOBOND@{NOBOND}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const int {\bf NFcore::Molecule::NOBOND} = 0\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1Molecule_2b8a424459016c1e580029e7170ce167}


\index{NFcore::Molecule@{NFcore::Molecule}!NOINDEX@{NOINDEX}}
\index{NOINDEX@{NOINDEX}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const int {\bf NFcore::Molecule::NOINDEX} = -1\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1Molecule_df16a8aa5b8b53462e2d569eec7f2e87}


\index{NFcore::Molecule@{NFcore::Molecule}!isPrepared@{isPrepared}}
\index{isPrepared@{isPrepared}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}bool {\bf NFcore::Molecule::isPrepared}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_74d0c636185f07f1d8dc8fe75f67bc5f}


\index{NFcore::Molecule@{NFcore::Molecule}!ID\_\-complex@{ID\_\-complex}}
\index{ID\_\-complex@{ID\_\-complex}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int {\bf NFcore::Molecule::ID\_\-complex}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_4f60e43c6a3dd9fe030dbb46e4cecec3}


\index{NFcore::Molecule@{NFcore::Molecule}!ID\_\-type@{ID\_\-type}}
\index{ID\_\-type@{ID\_\-type}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int {\bf NFcore::Molecule::ID\_\-type}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_8d3189072332d25bb33310dba5018a6e}


\index{NFcore::Molecule@{NFcore::Molecule}!ID\_\-unique@{ID\_\-unique}}
\index{ID\_\-unique@{ID\_\-unique}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int {\bf NFcore::Molecule::ID\_\-unique}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_df1361fab7ec14d70ee6956f0a3aeb1b}


\index{NFcore::Molecule@{NFcore::Molecule}!listId@{listId}}
\index{listId@{listId}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int {\bf NFcore::Molecule::listId}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_6910e617031aff17cbe1f33d1bf763b8}


\index{NFcore::Molecule@{NFcore::Molecule}!uniqueIdCount@{uniqueIdCount}}
\index{uniqueIdCount@{uniqueIdCount}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int {\bf Molecule::uniqueIdCount} = 0\hspace{0.3cm}{\tt  [static, protected]}}\label{classNFcore_1_1Molecule_48087dabb110f4ca4bcb40cae1916f7d}


\index{NFcore::Molecule@{NFcore::Molecule}!parentMoleculeType@{parentMoleculeType}}
\index{parentMoleculeType@{parentMoleculeType}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf MoleculeType}$\ast$ {\bf NFcore::Molecule::parentMoleculeType}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_ef848f04c27d380beb9044880f473268}


\index{NFcore::Molecule@{NFcore::Molecule}!useComplex@{useComplex}}
\index{useComplex@{useComplex}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}bool {\bf NFcore::Molecule::useComplex}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_63f93bdf7d7245f3fb58464338123bfe}


\index{NFcore::Molecule@{NFcore::Molecule}!component@{component}}
\index{component@{component}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ {\bf NFcore::Molecule::component}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_99d853296129fe8ec10967f40a05f683}


\index{NFcore::Molecule@{NFcore::Molecule}!numOfComponents@{numOfComponents}}
\index{numOfComponents@{numOfComponents}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int {\bf NFcore::Molecule::numOfComponents}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_d4eaff2cd6a7330fb368febe44cf0566}


\index{NFcore::Molecule@{NFcore::Molecule}!bond@{bond}}
\index{bond@{bond}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf Molecule}$\ast$$\ast$ {\bf NFcore::Molecule::bond}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_da5a46cb5da967a564bbee5ded5ff26f}


\index{NFcore::Molecule@{NFcore::Molecule}!indexOfBond@{indexOfBond}}
\index{indexOfBond@{indexOfBond}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ {\bf NFcore::Molecule::indexOfBond}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_8d794a2cc6d62ae44a808eb6338b5168}


\index{NFcore::Molecule@{NFcore::Molecule}!localFunctionValues@{localFunctionValues}}
\index{localFunctionValues@{localFunctionValues}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}double$\ast$ {\bf NFcore::Molecule::localFunctionValues}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_672b2d6623ef78af5ae2fabd55bebdfc}


\index{NFcore::Molecule@{NFcore::Molecule}!isObservable@{isObservable}}
\index{isObservable@{isObservable}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}bool$\ast$ {\bf NFcore::Molecule::isObservable}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_93d13a4e29d5e6b86a9d9302dde699d5}


\index{NFcore::Molecule@{NFcore::Molecule}!rxnListMappingId@{rxnListMappingId}}
\index{rxnListMappingId@{rxnListMappingId}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ {\bf NFcore::Molecule::rxnListMappingId}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_3dbaf63fe81ddc0bf6f183570d4a2a1c}


\index{NFcore::Molecule@{NFcore::Molecule}!nReactions@{nReactions}}
\index{nReactions@{nReactions}!NFcore::Molecule@{NFcore::Molecule}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}int {\bf NFcore::Molecule::nReactions}\hspace{0.3cm}{\tt  [protected]}}\label{classNFcore_1_1Molecule_d9e264d48c45c3e11e668d4014241359}




The documentation for this class was generated from the following files:\begin{CompactItemize}
\item 
/home/msneddon/eclipse/ganymede\_\-cpp/workspace/NFsim\_\-svn/src/NFcore/{\bf NFcore.hh}\item 
/home/msneddon/eclipse/ganymede\_\-cpp/workspace/NFsim\_\-svn/src/NFcore/{\bf molecule.cpp}\end{CompactItemize}
